Package ffx.numerics.estimator

Class EstimateBootstrapper

java.lang.Object
ffx.numerics.estimator.EstimateBootstrapper
public class EstimateBootstrapper extends Object
Bootstrap Free Energy Estimate.

  • Constructor Summary

    Constructors
    Constructor
    Description
    EstimateBootstrapper(BootstrappableEstimator estimator)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    bootstrap(long trials)
    Perform bootstrap analysis.
    void
    bootstrap(long trials, long logInterval)
    Perform bootstrap analysis.
    SummaryStatistics[]
    getBootstrapEnthalpyResults()
    Get Bootstrap Free Energy results for each window.
    static int[]
    getBootstrapIndices(int length)
    Gets randomized bootstrap indices; ensures there are at least two distinct indices.
    static int[]
    getBootstrapIndices(int length, Random random)
    Gets randomized bootstrap indices; ensures there are at least two distinct indices.
    static int[]
    getBootstrapIndices(int length, Random random, int minDistinct)
    Gets randomized bootstrap indices; ensures there are at least a few distinct indices.
    double[]
    getEnthalpy()
    Get bootstrap enthalpy estimate for each window.
    double[]
    getEnthalpyUncertainty()
    Get the enthalpy standard deviation estimate from bootstrap analysis for each window.
    double[]
    getEnthalpyVariance()
    Get the enthalpy variance estimate from bootstrap analysis for each window.
    double[]
    getFE()
    Get bootstrap free energy estimate for each window.
    double
    getTotalEnthalpy()
    Get the total enthalpy estimate from bootstrap analysis.
    double
    getTotalEnthalpy(double[] enthalpy)
    Get the total enthalpy estimate from per window bootstrap analysis.
    double
    getTotalEnthalpyUncertainty()
    Get the total enthalpy variance estimate from bootstrap analysis.
    double
    getTotalEnthalpyUncertainty(double[] var)
    Get the total enthalpy estimate from per window bootstrap analysis.
    double
    getTotalFE()
    Get the total free energy difference estimate from bootstrap analysis.
    double
    getTotalFE(double[] fe)
    Get the total free energy difference estimate from per window bootstrap analysis.
    double
    getTotalUncertainty()
    Get the total free energy difference variance estimate from bootstrap analysis.
    double
    getTotalUncertainty(double[] var)
    Get the total free energy difference estimate from per window bootstrap analysis.
    double[]
    getUncertainty()
    Get the free energy difference standard deviation estimate from bootstrap analysis for each window.
    double[]
    getVariance()
    Get the free energy difference variance estimate from bootstrap analysis for each window.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

  • Method Details

    • getBootstrapIndices

      public static int[] getBootstrapIndices(int length)
      Gets randomized bootstrap indices; ensures there are at least two distinct indices.
      Parameters:
      length - Number of random indices to generate in range [0,length)
      Returns:
      Randomized indices.

    • getBootstrapIndices

      public static int[] getBootstrapIndices(int length, Random random)
      Gets randomized bootstrap indices; ensures there are at least two distinct indices.
      Parameters:
      length - Number of random indices to generate in range [0,length)
      random - Source of randomness.
      Returns:
      Randomized indices.

    • getBootstrapIndices

      public static int[] getBootstrapIndices(int length, Random random, int minDistinct)
      Gets randomized bootstrap indices; ensures there are at least a few distinct indices.
      Parameters:
      length - Number of random indices to generate in range [0,length)
      random - Source of randomness.
      minDistinct - Minimum number of distinct indices.
      Returns:
      Randomized indices.

    • getBootstrapEnthalpyResults

      public SummaryStatistics[] getBootstrapEnthalpyResults()
      Get Bootstrap Free Energy results for each window.
      Returns:
      Bootstrap Enthalpy results for each window.

    • bootstrap

      public void bootstrap(long trials)
      Perform bootstrap analysis.
      Parameters:
      trials - Number of trials.

    • bootstrap

      public void bootstrap(long trials, long logInterval)
      Perform bootstrap analysis.
      Parameters:
      trials - Number of trials.
      logInterval - Interval between logging statements.

    • getFE

      public double[] getFE()
      Get bootstrap free energy estimate for each window.
      Returns:
      Return the bootstrap free energy difference estimate for each window.

    • getEnthalpy

      public double[] getEnthalpy()
      Get bootstrap enthalpy estimate for each window.
      Returns:
      Return the bootstrap enthalpy estimate for each window.

    • getTotalFE

      public double getTotalFE()
      Get the total free energy difference estimate from bootstrap analysis.
      Returns:
      The total free energy difference estimate.

    • getTotalEnthalpy

      public double getTotalEnthalpy()
      Get the total enthalpy estimate from bootstrap analysis.
      Returns:
      The total enthalpy estimate.

    • getTotalFE

      public double getTotalFE(double[] fe)
      Get the total free energy difference estimate from per window bootstrap analysis.
      Parameters:
      fe - The free energy difference estimate for each window.
      Returns:
      The total free energy difference estimate from bootstrap analysis.

    • getTotalEnthalpy

      public double getTotalEnthalpy(double[] enthalpy)
      Get the total enthalpy estimate from per window bootstrap analysis.
      Parameters:
      enthalpy - The enthalpy estimate for each window.
      Returns:
      The total enthalpy difference estimate from bootstrap analysis.

    • getTotalUncertainty

      public double getTotalUncertainty()
      Get the total free energy difference variance estimate from bootstrap analysis.
      Returns:
      The total free energy difference variance estimate.

    • getTotalUncertainty

      public double getTotalUncertainty(double[] var)
      Get the total free energy difference estimate from per window bootstrap analysis.
      Parameters:
      var - The free energy difference variance estimate (not uncertainty) for each window.
      Returns:
      The total free energy difference variance estimate from bootstrap analysis.

    • getTotalEnthalpyUncertainty

      public double getTotalEnthalpyUncertainty()
      Get the total enthalpy variance estimate from bootstrap analysis.
      Returns:
      The total enthalpy variance estimate.

    • getTotalEnthalpyUncertainty

      public double getTotalEnthalpyUncertainty(double[] var)
      Get the total enthalpy estimate from per window bootstrap analysis.
      Parameters:
      var - The enthalpy variance estimate (not uncertainty) for each window.
      Returns:
      The total enthalpy variance estimate from bootstrap analysis.

    • getUncertainty

      public double[] getUncertainty()
      Get the free energy difference standard deviation estimate from bootstrap analysis for each window.
      Returns:
      Returns free energy difference standard deviation estimate for each window.

    • getEnthalpyUncertainty

      public double[] getEnthalpyUncertainty()
      Get the enthalpy standard deviation estimate from bootstrap analysis for each window.
      Returns:
      Returns enthalpy standard deviation estimate for each window.

    • getVariance

      public double[] getVariance()
      Get the free energy difference variance estimate from bootstrap analysis for each window.
      Returns:
      Returns free energy difference variance estimate for each window.

    • getEnthalpyVariance

      public double[] getEnthalpyVariance()
      Get the enthalpy variance estimate from bootstrap analysis for each window.
      Returns:
      Returns enthalpy variance estimate for each window.